Loops were firstly called using Mustache. Afterwards, a union of significantly called loops in each condition (M1, M4 and NTC) was used for differential analysis using a modified DESeq2 approach via HiCDCPlus. Knockdown samples (M1 and M4) were pooled together. Loops can be visualized using Hi-C contact maps found here.
Download diff_final.csvThe number of significant loops (FDR < 0.05) is reported in each condition.
Logfold change is MED4KD over NTC

Using a cutoff of 50 normalized mean counts

Using a cutoff of 100 normalized mean counts

